Integrated multi-omics single cell atlas of the human retina.

TitleIntegrated multi-omics single cell atlas of the human retina.
Publication TypeJournal Article
Year of Publication2023
AuthorsLi, J, Wang, J, Ibarra, IL, Cheng, X, Luecken, MD, Lu, J, Monavarfeshani, A, Yan, W, Zheng, Y, Zuo, Z, Colborn, SLynn Zayas, Cortez, BSarahi, Owen, LA, Tran, NM, Shekhar, K, Sanes, JR, J Stout, T, Chen, S, Li, Y, DeAngelis, MM, Theis, FJ, Chen, R
JournalRes Sq
Date Published2023 Nov 17

Single-cell sequencing has revolutionized the scale and resolution of molecular profiling of tissues and organs. Here, we present an integrated multimodal reference atlas of the most accessible portion of the mammalian central nervous system, the retina. We compiled around 2.4 million cells from 55 donors, including 1.4 million unpublished data points, to create a comprehensive human retina cell atlas (HRCA) of transcriptome and chromatin accessibility, unveiling over 110 types. Engaging the retina community, we annotated each cluster, refined the Cell Ontology for the retina, identified distinct marker genes, and characterized cis-regulatory elements and gene regulatory networks (GRNs) for these cell types. Our analysis uncovered intriguing differences in transcriptome, chromatin, and GRNs across cell types. In addition, we modeled changes in gene expression and chromatin openness across gender and age. This integrated atlas also enabled the fine-mapping of GWAS and eQTL variants. Accessible through interactive browsers, this multimodal cross-donor and cross-lab HRCA, can facilitate a better understanding of retinal function and pathology.

Alternate JournalRes Sq
PubMed ID38014002
PubMed Central IDPMC10680922
Grant ListP30 EY002687 / EY / NEI NIH HHS / United States
R01 EY012543 / EY / NEI NIH HHS / United States
U01 MH105960 / MH / NIMH NIH HHS / United States
S10 OD023469 / OD / NIH HHS / United States
R21 EY028633 / EY / NEI NIH HHS / United States
R01 EY027784 / EY / NEI NIH HHS / United States
R01 EY032136 / EY / NEI NIH HHS / United States